Cat keeps scratching ears and shaking head

My cat's ears seem to be bothering him. He frequently scratches them and also shakes his head. The vet suggested that it may be food allergies (he mentioned fish), so I switched my cat to California Natural Grain-Free Chicken, which has nothing but chicken, peas, sunflower oil, and vitamins and minerals in it. The problem persisted, so I took him back to the vet, who prescribed him Atopica. This has not worked. The vet did suggest steroids, but wanted to try Atopica first because of the negative side effects of steroids. The vet thought that it may be environmental allergies. The only other thing that I can think of is stress from a recent move, but I cannot see how stress and ears are connected.

Has anyone ever experienced this before? Thank you

Has he been checked for ear mites? They're the number one cause of ear irritation in cats, and can cause permanent damage if left untreated.
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He had earmites when I first got him from the shelter, but they were treated. I have visited the vet three times since then for vaccines and this new ear issue, and the vet checked every time for earmites and said that my cat has no ear mites or parasites.

The only other thought I have to try is Bach's Flower Remedies Crab Apple. It's meant to be good for skin irritation. I've never used it for that myself, but I've had great success with other Bach Flower Remedies. It's definitely worth trying though.

Stress can trigger skin issues - eczema can often be triggered or worsened by stress, so taking stress busting measures is well worth trying.